Questions on loop modelling
My target sequence has two insertions at 2 loop regions (14aa, 9aa) when compare to my template structure. I have three questions:
1. Since 12aa is the limit of loop modelling, is that viable to build a "model" with the "template sequence plus 2 aa of the "target" insertion, then use this "template +2aa" model as template for building the model of the target????
2. The residues flanking the insertions also belong to the loop regions (of the template), so, my question is, when we do loop modelling, do we need to model the whole piece of loop for accuracy??
3. When we generate loop models, do you model one loop and then the other? Since I have two loop regions, I wonder if I should build (~500) models for one regions and then another set for the other region? Does one loop region actually affect the conformation of the other loop? Do you think it's necessary to build them both at the same time?
Thank you very much for answering the questions. Have a great day.
Sincerely, Jasmine
--------------------------------- Do you Yahoo!? Next-gen email? Have it all with the all-new Yahoo! Mail Beta.
hori koshii wrote: > 1. Since 12aa is the limit of loop modelling, is that viable to build a > "model" with the "template sequence plus 2 aa of the "target" > insertion, then use this "template +2aa" model as template for building > the model of the target????
There is no 'limit' to loop modeling, but the longer the loop, the larger the space that must be sampled. Your approach doesn't solve the problem, because you still have to sample a 14aa loop, whether you do it all at once or in chunks. You can certainly use loop modeling for 14aa insertions, but you should be aware that the predictions aren't as reliable as those for a shorter insertion.
> 2. The residues flanking the insertions also belong to the loop regions > (of the template), so, my question is, when we do loop modelling, do we > need to model the whole piece of loop for accuracy??
If you think they need to move, you need to include them. Modeller uses the residues immediately adjacent to the loop region to anchor the loop (this reduces the space that must be searched) and so does not move them.
> 3. When we generate loop models, do you model one loop and then the > other? Since I have two loop regions, I wonder if I should build (~500) > models for one regions and then another set for the other region? Does > one loop region actually affect the conformation of the other loop? Do > you think it's necessary to build them both at the same time?
That depends on how close the loops are in space. If they are far apart, you can certainly model them both at once.
Ben Webb, Modeller Caretaker
Modeller Caretaker wrote: > hori koshii wrote: >> 3. When we generate loop models, do you model one loop and then the >> other? > That depends on how close the loops are in space. If they are far apart, > you can certainly model them both at once.
Oops, I actually meant: If the two loops are close together, you certainly _should_ model them both at once. If they are far apart, you can model them together or separately, but you should certainly treat the two loops separately when you assess and rank them - a good model for one loop does not necessarily mean a good model for the other, in this case.
Ben Webb, Modeller Caretaker
participants (2)
-
hori koshii -
Modeller Caretaker